Uses of Interface
fern.network.AmountManager

Packages that use AmountManager

Package	Description
fern.network
fern.network.modification
fern.network.sbml
org.simulator.sbml	Classes for storing and interpreting an SBML model.

Uses of AmountManager in fern.network

Classes in fern.network that implement AmountManager

Modifier and Type	Class and Description
class	ConstantAmountManager
class	DefaultAmountManager Default implementation of an amount manager, that stores the amounts in arrays.

Methods in fern.network that return AmountManager

Modifier and Type	Method and Description
AmountManager	Network.getAmountManager() Gets the AmountManager for this network.
AmountManager	AbstractNetworkImpl.getAmountManager()

Methods in fern.network with parameters of type AmountManager

Modifier and Type	Method and Description
double	AbstractKineticConstantPropensityCalculator.calculatePartialDerivative(int reaction, AmountManager amount, int reactantIndex, double volume) Calculates partial differentials of the propensity functions for the tau leaping methods.
double	PartialDerivativePropensityCalculator.calculatePartialDerivative(int reaction, AmountManager amount, int reactantIndex, double volume) Calculates partial differentials of the propensity functions for the tau leaping methods.
double	PropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim) Calculates the propensity for a reaction given the amounts of the AmountManager.
double	AbstractKineticConstantPropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim) Calculates the propensity for reaction by the formula h*c, where c is the kinetic constant for reaction and h is the number of distinct molecular reactant combinations for reaction.

Uses of AmountManager in fern.network.modification

Methods in fern.network.modification that return AmountManager

Modifier and Type	Method and Description
AmountManager	ModifierNetwork.getAmountManager() Gets the AmountManager of the original network.
AmountManager	ReversibleNetwork.getAmountManager() Gets the AmountManager for the modified network.
AmountManager	CatalysedNetwork.getAmountManager()
AmountManager	ExtractSubNetwork.getAmountManager() Gets the AmountManager for the extracted subnet.

Uses of AmountManager in fern.network.sbml

Methods in fern.network.sbml with parameters of type AmountManager

Modifier and Type	Method and Description
double	MathTree.calculate(AmountManager amount, Simulator sim) Evaluate the MathTree.
double	SBMLPropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim)

Uses of AmountManager in org.simulator.sbml

Methods in org.simulator.sbml with parameters of type AmountManager

Modifier and Type	Method and Description
void	SBMLinterpreter.updateSpeciesConcentration(AmountManager amountManager) Updates the species concentration as per the updated values in the AmountManager.